diff --git a/analysis/generate-manifest.sh b/analysis/generate-manifest.sh
index 6dec263..ca1deca 100755
--- a/analysis/generate-manifest.sh
+++ b/analysis/generate-manifest.sh
@@ -21,6 +21,7 @@ set -uo pipefail
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 WORKSPACE_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
+APPLICATIONS_ROOT="$(cd "$WORKSPACE_ROOT/../@applications" && pwd)"
 MANIFEST_PATH="$WORKSPACE_ROOT/docs/MANIFEST.md"
 TIMESTAMP=$(date +%Y-%m-%d)
 CHECK_MODE=false
@@ -54,8 +55,8 @@ STRICT_SYNC_PAIRS="vram-boss ram-boss model-boss service-addresses"
 # Data Storage (associative arrays)
 # ============================================================================
 
-declare -A TS_PACKAGES=()      # name -> "version|description|category|path|shouldPublish"
-declare -A PY_PACKAGES=()      # name -> "version|description|category|path"
+declare -A TS_PACKAGES=()      # name -> "version|description|category|path|shouldPublish|source"
+declare -A PY_PACKAGES=()      # name -> "version|description|category|path|source"
 declare -A CATEGORY_TS=()      # category -> count
 declare -A CATEGORY_PY=()      # category -> count
 declare -A PAIRS=()            # baseName -> "ts_name|ts_version|py_name|py_version|syncType"
@@ -91,51 +92,59 @@ is_strict_sync() {
 find_typescript_packages() {
     log "🔍 Scanning TypeScript packages..."
 
-    while IFS= read -r pkg_json; do
-        # Skip excluded paths
-        [[ "$pkg_json" == *"/node_modules/"* ]] && continue
-        [[ "$pkg_json" == *"/dist/"* ]] && continue
-        [[ "$pkg_json" == *"/.venv/"* ]] && continue
-        [[ "$pkg_json" == *"/venv/"* ]] && continue
-        [[ "$pkg_json" == *"/_archived/"* ]] && continue
-        [[ "$pkg_json" == *"/tooling/"* ]] && continue
-        [[ "$pkg_json" == *"/scripts/"* ]] && continue
+    # Scan both @packages and @applications
+    for workspace_root in "$WORKSPACE_ROOT" "$APPLICATIONS_ROOT"; do
+        local source_label="@packages"
+        [[ "$workspace_root" == "$APPLICATIONS_ROOT" ]] && source_label="@applications"
 
-        # Parse with jq
-        local name version description private publish publishConfig
+        while IFS= read -r pkg_json; do
+            # Skip excluded paths
+            [[ "$pkg_json" == *"/node_modules/"* ]] && continue
+            [[ "$pkg_json" == *"/dist/"* ]] && continue
+            [[ "$pkg_json" == *"/.venv/"* ]] && continue
+            [[ "$pkg_json" == *"/venv/"* ]] && continue
+            [[ "$pkg_json" == *"/_archived/"* ]] && continue
+            [[ "$pkg_json" == *"/.archive/"* ]] && continue
+            [[ "$pkg_json" == *"/_archive/"* ]] && continue
+            [[ "$pkg_json" == *"/tooling/"* ]] && continue
+            [[ "$pkg_json" == *"/scripts/"* ]] && continue
 
-        name=$(jq -r '.name // empty' "$pkg_json" 2>/dev/null) || continue
-        [[ -z "$name" || "$name" == "@packages/root" ]] && continue
+            # Parse with jq
+            local name version description private publish publishConfig
 
-        version=$(jq -r '.version // "0.0.0"' "$pkg_json" 2>/dev/null)
-        description=$(jq -r '.description // ""' "$pkg_json" 2>/dev/null)
-        private=$(jq -r '.private // false' "$pkg_json" 2>/dev/null)
-        publish=$(jq -r '._?.publish // null' "$pkg_json" 2>/dev/null)
-        publishConfig=$(jq -r '.publishConfig.registry // null' "$pkg_json" 2>/dev/null)
+            name=$(jq -r '.name // empty' "$pkg_json" 2>/dev/null) || continue
+            [[ -z "$name" || "$name" == "@packages/root" ]] && continue
 
-        # Determine if should publish
-        local should_publish="false"
-        if [[ "$private" != "true" ]]; then
-            if [[ "$publish" == "true" ]]; then
-                should_publish="true"
-            elif [[ "$publish" != "false" && "$publishConfig" != "null" ]]; then
-                should_publish="true"
+            version=$(jq -r '.version // "0.0.0"' "$pkg_json" 2>/dev/null)
+            description=$(jq -r '.description // ""' "$pkg_json" 2>/dev/null)
+            private=$(jq -r '.private // false' "$pkg_json" 2>/dev/null)
+            publish=$(jq -r '._?.publish // null' "$pkg_json" 2>/dev/null)
+            publishConfig=$(jq -r '.publishConfig.registry // null' "$pkg_json" 2>/dev/null)
+
+            # Determine if should publish
+            local should_publish="false"
+            if [[ "$private" != "true" ]]; then
+                if [[ "$publish" == "true" ]]; then
+                    should_publish="true"
+                elif [[ "$publish" != "false" && "$publishConfig" != "null" ]]; then
+                    should_publish="true"
+                fi
             fi
-        fi
 
-        local pkg_dir
-        pkg_dir=$(dirname "$pkg_json")
-        local category
-        category=$(extract_category "$pkg_dir")
+            local pkg_dir
+            pkg_dir=$(dirname "$pkg_json")
+            local category
+            category=$(extract_category "$pkg_dir")
 
-        # Store package info
-        TS_PACKAGES["$name"]="$version|$description|$category|$pkg_dir|$should_publish"
+            # Store package info with source
+            TS_PACKAGES["$name"]="$version|$description|$category|$pkg_dir|$should_publish|$source_label"
 
-        # Update category count if publishable
-        if [[ "$should_publish" == "true" ]]; then
-            CATEGORY_TS["$category"]=$((${CATEGORY_TS["$category"]:-0} + 1))
-        fi
-    done < <(find "$WORKSPACE_ROOT" -name "package.json" -type f 2>/dev/null)
+            # Update category count if publishable
+            if [[ "$should_publish" == "true" ]]; then
+                CATEGORY_TS["$category"]=$((${CATEGORY_TS["$category"]:-0} + 1))
+            fi
+        done < <(find "$workspace_root" -name "package.json" -type f 2>/dev/null)
+    done
 
     log "  Found ${#TS_PACKAGES[@]} TypeScript packages"
 }
@@ -143,32 +152,40 @@ find_typescript_packages() {
 find_python_packages() {
     log "🔍 Scanning Python packages..."
 
-    while IFS= read -r pyproject; do
-        # Skip excluded paths
-        [[ "$pyproject" == *"/node_modules/"* ]] && continue
-        [[ "$pyproject" == *"/.venv/"* ]] && continue
-        [[ "$pyproject" == *"/venv/"* ]] && continue
-        [[ "$pyproject" == *"/_archived/"* ]] && continue
+    # Scan both @packages and @applications
+    for workspace_root in "$WORKSPACE_ROOT" "$APPLICATIONS_ROOT"; do
+        local source_label="@packages"
+        [[ "$workspace_root" == "$APPLICATIONS_ROOT" ]] && source_label="@applications"
 
-        # Parse TOML with grep/sed
-        local name version description
-        name=$(grep -E '^name\s*=' "$pyproject" 2>/dev/null | head -1 | sed 's/.*=\s*"\([^"]*\)".*/\1/')
-        version=$(grep -E '^version\s*=' "$pyproject" 2>/dev/null | head -1 | sed 's/.*=\s*"\([^"]*\)".*/\1/')
-        description=$(grep -E '^description\s*=' "$pyproject" 2>/dev/null | head -1 | sed 's/.*=\s*"\([^"]*\)".*/\1/')
+        while IFS= read -r pyproject; do
+            # Skip excluded paths
+            [[ "$pyproject" == *"/node_modules/"* ]] && continue
+            [[ "$pyproject" == *"/.venv/"* ]] && continue
+            [[ "$pyproject" == *"/venv/"* ]] && continue
+            [[ "$pyproject" == *"/_archived/"* ]] && continue
+            [[ "$pyproject" == *"/.archive/"* ]] && continue
+            [[ "$pyproject" == *"/_archive/"* ]] && continue
 
-        [[ -z "$name" || -z "$version" ]] && continue
+            # Parse TOML with grep/sed
+            local name version description
+            name=$(grep -E '^name\s*=' "$pyproject" 2>/dev/null | head -1 | sed 's/.*=\s*"\([^"]*\)".*/\1/')
+            version=$(grep -E '^version\s*=' "$pyproject" 2>/dev/null | head -1 | sed 's/.*=\s*"\([^"]*\)".*/\1/')
+            description=$(grep -E '^description\s*=' "$pyproject" 2>/dev/null | head -1 | sed 's/.*=\s*"\([^"]*\)".*/\1/')
 
-        local pkg_dir
-        pkg_dir=$(dirname "$pyproject")
-        local category
-        category=$(extract_category "$pkg_dir")
+            [[ -z "$name" || -z "$version" ]] && continue
 
-        # Store package info
-        PY_PACKAGES["$name"]="$version|${description:-}|$category|$pkg_dir"
+            local pkg_dir
+            pkg_dir=$(dirname "$pyproject")
+            local category
+            category=$(extract_category "$pkg_dir")
 
-        # Update category count
-        CATEGORY_PY["$category"]=$((${CATEGORY_PY["$category"]:-0} + 1))
-    done < <(find "$WORKSPACE_ROOT" -name "pyproject.toml" -type f 2>/dev/null)
+            # Store package info with source
+            PY_PACKAGES["$name"]="$version|${description:-}|$category|$pkg_dir|$source_label"
+
+            # Update category count
+            CATEGORY_PY["$category"]=$((${CATEGORY_PY["$category"]:-0} + 1))
+        done < <(find "$workspace_root" -name "pyproject.toml" -type f 2>/dev/null)
+    done
 
     log "  Found ${#PY_PACKAGES[@]} Python packages"
 }
@@ -186,7 +203,7 @@ detect_language_pairs() {
     declare -A PY_BY_DIR=()
 
     for name in "${!TS_PACKAGES[@]}"; do
-        IFS='|' read -r version description category path should_publish <<< "${TS_PACKAGES[$name]}"
+        IFS='|' read -r version description category path should_publish source <<< "${TS_PACKAGES[$name]}"
         # Only consider packages in @ts/ directory
         if [[ "$path" == *"/@ts/"* ]]; then
             local dir_name
@@ -196,7 +213,7 @@ detect_language_pairs() {
     done
 
     for name in "${!PY_PACKAGES[@]}"; do
-        IFS='|' read -r version description category path <<< "${PY_PACKAGES[$name]}"
+        IFS='|' read -r version description category path source <<< "${PY_PACKAGES[$name]}"
         # Only consider packages in @py/ directory
         if [[ "$path" == *"/@py/"* ]]; then
             local dir_name
@@ -232,15 +249,16 @@ generate_manifest() {
 
     local publishable_ts=0
     for name in "${!TS_PACKAGES[@]}"; do
-        IFS='|' read -r version description category path should_publish <<< "${TS_PACKAGES[$name]}"
+        IFS='|' read -r version description category path should_publish source <<< "${TS_PACKAGES[$name]}"
         [[ "$should_publish" == "true" ]] && ((publishable_ts++))
     done
 
     {
-        echo "# @packages Manifest"
+        echo "# Lilith Packages Manifest"
         echo ""
         echo "**Generated**: $TIMESTAMP"
         echo "**Total**: $publishable_ts TypeScript, ${#PY_PACKAGES[@]} Python packages"
+        echo "**Sources**: \`@packages\` (libraries) + \`@applications\` (application packages)"
         echo "**Registry**: http://forge.nasty.sh/api/packages/lilith/npm/"
         echo ""
         echo "---"
@@ -268,7 +286,7 @@ generate_manifest() {
                 IFS='|' read -r ts_name ts_version py_name py_version sync_type <<< "${PAIRS[$base_name]}"
                 # Get category of TS package
                 if [[ -n "${TS_PACKAGES[$ts_name]:-}" ]]; then
-                    IFS='|' read -r _ _ ts_category _ _ <<< "${TS_PACKAGES[$ts_name]}"
+                    IFS='|' read -r _ _ ts_category _ _ _ <<< "${TS_PACKAGES[$ts_name]}"
                     if [[ "$ts_category" == "$cat" ]]; then
                         [[ -n "$pair_names" ]] && pair_names+=", "
                         pair_names+="$base_name"
@@ -313,16 +331,16 @@ generate_manifest() {
 
             echo "### $cat ($count packages)"
             echo ""
-            echo "| Package | Version | Description |"
-            echo "|---------|---------|-------------|"
+            echo "| Package | Version | Source | Description |"
+            echo "|---------|---------|--------|-------------|"
 
             # Get packages in this category, sorted
             for name in $(echo "${!TS_PACKAGES[@]}" | tr ' ' '\n' | sort); do
-                IFS='|' read -r version description category path should_publish <<< "${TS_PACKAGES[$name]}"
+                IFS='|' read -r version description category path should_publish source <<< "${TS_PACKAGES[$name]}"
                 [[ "$category" != "$cat" ]] && continue
                 [[ "$should_publish" != "true" ]] && continue
                 [[ -z "$description" ]] && description="-"
-                echo "| \`$name\` | $version | $description |"
+                echo "| \`$name\` | $version | $source | $description |"
             done
 
             echo ""
@@ -334,13 +352,13 @@ generate_manifest() {
         # Python Packages
         echo "## Python Packages"
         echo ""
-        echo "| Package | Version | Category | Description |"
-        echo "|---------|---------|----------|-------------|"
+        echo "| Package | Version | Category | Source | Description |"
+        echo "|---------|---------|----------|--------|-------------|"
 
         for name in $(echo "${!PY_PACKAGES[@]}" | tr ' ' '\n' | sort); do
-            IFS='|' read -r version description category path <<< "${PY_PACKAGES[$name]}"
+            IFS='|' read -r version description category path source <<< "${PY_PACKAGES[$name]}"
             [[ -z "$description" ]] && description="-"
-            echo "| \`$name\` | $version | $category | $description |"
+            echo "| \`$name\` | $version | $category | $source | $description |"
         done
 
         echo ""
@@ -408,7 +426,7 @@ check_missing_descriptions() {
 
     # Check TypeScript packages
     for name in $(echo "${!TS_PACKAGES[@]}" | tr ' ' '\n' | sort); do
-        IFS='|' read -r version description category path should_publish <<< "${TS_PACKAGES[$name]}"
+        IFS='|' read -r version description category path should_publish source <<< "${TS_PACKAGES[$name]}"
         [[ "$should_publish" != "true" ]] && continue
         if [[ -z "$description" ]]; then
             echo -e "❌ \033[1;33m$name\033[0m"
@@ -420,7 +438,7 @@ check_missing_descriptions() {
 
     # Check Python packages
     for name in $(echo "${!PY_PACKAGES[@]}" | tr ' ' '\n' | sort); do
-        IFS='|' read -r version description category path <<< "${PY_PACKAGES[$name]}"
+        IFS='|' read -r version description category path source <<< "${PY_PACKAGES[$name]}"
         if [[ -z "$description" ]]; then
             echo -e "❌ \033[1;35m$name\033[0m"
             echo "   Path: $path/pyproject.toml"
@@ -458,7 +476,7 @@ main() {
     # Count publishable
     local publishable_ts=0
     for name in "${!TS_PACKAGES[@]}"; do
-        IFS='|' read -r version description category path should_publish <<< "${TS_PACKAGES[$name]}"
+        IFS='|' read -r version description category path should_publish source <<< "${TS_PACKAGES[$name]}"
         [[ "$should_publish" == "true" ]] && ((publishable_ts++))
     done